Introduction

Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment, called MSQuant, which allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net .

Publications

  1. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics.
    Cite this
    Mortensen P, Gouw JW, Olsen JV, Ong SE, Rigbolt KT, Bunkenborg J, Cox J, Foster LJ, Heck AJ, Blagoev B, Andersen JS, Mann M, 2010-01-01 - Journal of proteome research

Credits

  1. Peter Mortensen
    Developer

  2. Joost W Gouw
    Developer

  3. Jesper V Olsen
    Developer

  4. Shao-En Ong
    Developer

  5. Kristoffer T G Rigbolt
    Developer

  6. Jakob Bunkenborg
    Developer

  7. Jürgen Cox
    Developer

  8. Leonard J Foster
    Developer

  9. Albert J R Heck
    Developer

  10. Blagoy Blagoev
    Developer

  11. Jens S Andersen
    Developer

  12. Matthias Mann
    Investigator

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Summary
AccessionBT005680
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByMatthias Mann